NAME

Bio::PopGen::PopulationI - Interface for Populations

SYNOPSIS

# Get Bio::PopGen::PopulationI object somehow, like
# from Bio::Population::Population

print "name is ", $population->name(), "\n";
print "source is ", $population->source(), "\n";
print "description is ", $population->description(), "\n";

print "For marker $markername:\n";
foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) {
    print "Individual ", $genotype->individual_id, " genotype alleles are ",
    join(',', $genotype->get_Alleles()), "\n";
}
# get a marker with allele frequencies calculated from the population
my $marker = $population->get_Marker($markername); 
my %af = $marker->get_Allele_Frequencies;
foreach my $allele ( keys %af ) {
    print "$allele $af{$allele}\n";
}

DESCRIPTION

This interface describes the basics of a population. One can use this object to get the genotypes of specific individuals, only those individuals which have a certain marker, or create a marker with allele frequency information.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

name

Title   : name
Usage   : my $name = $pop->name
Function: Get the population name
Returns : string representing population name
Args    : [optional] string representing population name

description

Title   : description
Usage   : my $description = $pop->description
Function: Get the population description
Returns : string representing population description
Args    : [optional] string representing population description

source

Title   : source
Usage   : my $source = $pop->source
Function: Get the population source
Returns : string representing population source
Args    : [optional] string representing population source

annotation

Title   : annotation
Usage   : my $annotation_collection = $pop->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this population
Returns : Bio::AnnotationCollectionI object
Args    : [optional set] Bio::AnnotationCollectionI object

get_Individuals

Title   : get_Individuals
Usage   : my @inds = $pop->get_Individuals();
Function: Return the individuals, alternatively restrict by a criteria
Returns : Array of L<Bio::PopGen::IndividualI> objects
Args    : none if want all the individuals OR,
          -unique_id => To get an individual with a specific id
          -marker    => To only get individuals which have a genotype specific
                       for a specific marker name

get_Genotypes

Title   : get_Genotypes
Usage   : my @genotypes = $pop->get_Genotypes(-marker => $name)
Function: Get the genotypes for all the individuals for a specific
          marker name
Returns : Array of L<Bio::PopGen::GenotypeI> objects
Args    : -marker => name of the marker

get_Marker

Title   : get_Marker
Usage   : my $marker = $population->get_Marker($name)
Function: Get a Bio::PopGen::Marker object based on this population
Returns : L<Bio::PopGen::MarkerI> object
Args    : name of the marker

get_marker_names

Title   : get_marker_names
Usage   : my @names = $pop->get_marker_names;
Function: Get the names of the markers
Returns : Array of strings
Args    : none

get_Markers

Title   : get_Markers
Usage   : my @markers = $pop->get_Markers();
Function: Will retrieve a list of instantiated MarkerI objects 
          for a population.  This is a convience method combining
          get_marker_names with get_Marker
Returns : List of array of Bio::PopGen::MarkerI objects
Args    : none

get_number_individuals

Title   : get_number_individuals
Usage   : my $count = $pop->get_number_individuals;
Function: Get the count of the number of individuals
Returns : integer >= 0
Args    : [optional] marker name, will return a count of the number
          of individuals which have this marker

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq